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The Sox family plays essential roles as transcription factors in vertebrates; however, little is known about the Sox family in Lutraria sieboldii. L. sieboldii are pleasant to eat with a short growth cycle and have become one of the best bottom-seeded enrichment species in Guang Xi. In this study, Sox2 (named LsSox2) and Sox9 (named LsSox9) from L. sieboldii were cloned, and their expression patterns were analyzed. The length of the LsSox2 gene coding sequence was 1011 bp, encoding 336 amino acids, and LsSox9 was 1449 bp, encoding 482 amino acids. LsSox2 had its highest expression levels in the ovary, which were 356 times those in testis, whereas LsSox9 presented higher expression in testis, which was 6 times more highly expressed than in the ovary. LsSox2 exhibited the highest expression during the morula stage, which was 20 times that of the D-shaped larvae or zygote. LsSox9 exhibited two expression peaks, one at the four-cell stage and the other at the trochophore stage, while the lowest expression was in the zygote. LsSox9 was 73 times more highly expressed in the four-cell stage than in the zygote stage. During gonadal development, LsSox2 presented the highest expression in the mature ovary, which was 756 times more highly expressed than in mature testis. LsSox9 presented higher expression in testis at the emission stage which was 6 times more highly expressed than in the ovary. These results indicate that LsSox2 and LsSox9 may play important roles in embryonic and gonadal development.